We examined genomic DNA from 31 follicular neoplasms, 20 follicular carcinomas (FC) and 11 follicular adenomas (FA) for loss of heterozygosity (LOH) using PCR-based microsatellite polymorphisms for all chromosomal arms. Although there was a tendency for FC to exhibit a greater percent LOH on certain chromosomal arms than the FA, there was no statistically significant difference between LOH seen in PA. However, when we examined more closely the follicular neoplasms we found that there was a significant difference between the Hurthle cell variant of follicular carcinoma and Hurthle cell variant of follicular adenoma. We, therefore, further pursued this and found that Hurthle cell carcinomas (RC) had significantly greater chromosomal abnormalities than Hurthle cell adenomas (HA) on chromosomal a=Iq and 2p and that all Hurthle cell neoplasms (HN) had a significantly greater frequency of alterations on chromosomal arm lp compared to normal thyroid glands. In an attempt to further evaluate the role of these genetic alterations in Hurthle cell tumorigenesis, we examined chromosomal arms lp, Iq and 2p in 19 HC and 32 KA. More than 15 primers that flanked CA-repeat regions on each chromosomal arm were radiolabelled. DNA was PCR- amplified using the radiolabelled primers, and PCR products were separated by electrophoresis on 6% denaturing urea-polyacrylamide gels. Allelic loss was recorded if the signal intensity of one allele in informative cases was at least 50% decreased in the tumor DNA as compared to corresponding normal DNA; allelic gain was considered if additional bands were noted. Differences in allelic alterations were significantly greater in HC than HA by Fisher's exact test (p<0.05) at six loci 1p:D1S224,D1S207)(Iq:D1SI660)(2p:D2S1240,D2S1788,D2S1394). These results strongly support the thyroid tumor progression model and implicate chromosomal arms lp,lq,and 2p in the tumorigenesis of Hurthle cell neoplasms. Additional mapping of these regions is needed to further elucidate the underlying molecular genetic mechanisms responsible. Finally, because the differential diagnosis of follicular neoplasms still posed a clinical dilemma without solution, we pursued another molecular market, namely telomerase, to determine whether or not it would distinguish FA from PC. Telomerase activity was detected in 11 of 11 carcinomas, in 5 of 23 benign follicular adenomas and in none of 22 matched normal thyroid tissues. In this series the telomerase assay had a specificity of 74% and a sensitivity of 100%. Because of this preliminary data we have instituted a multi-institutional study looking at telomerase activity in the differential diagnosis of follicular neoplasms. And finally, because of the promising data with Hurthle cell neoplasms, we plan to further map the chromosomal regions that have abnormalities on lp, Iq and 2p in Hurthle cell carcinomas.